Not sure if the current version already allows that - but this is a common flaw with most Markdown note-taking software (I have around 8000 posts/notes spanning 16 years of hierarchies, some time-based and some context-based).
we're still using the dotted namespacing but we've also introduced the ability to export your notes to plain markdown (it inlines dendron specific markdown like note references to regular markdown). if you have folder based markdown, you can import them to dendron's format using our markdown importer and then export them to the same format as well (this is coming soon)
For me, this kind of note taking app ought to use folder names as topics or categories (dev/rust) and have an index.md (dev/rust/index.md) as an entry point, and some sub-documents/sub-sections in the same folder.
Also, many of these tools only go half way: they have folder support but instead of a "bag of posts" you have to put images in a "bag of media" folder, which is even worse sometimes...
I remember there is also a plugin which allows to use folder as notes, by loading a kind of index.md when opening the folder.
But what do you mean with "bag of media" folder?